[Swift-commit] r5942 - SwiftApps/CMTS/scaling

[davidk at ci.uchicago.edu]

Author: davidk
Date: 2012-09-20 16:05:59 -0500 (Thu, 20 Sep 2012)
New Revision: 5942

Modified:
   SwiftApps/CMTS/scaling/README
Log:
formatting


Modified: SwiftApps/CMTS/scaling/README
===================================================================
--- SwiftApps/CMTS/scaling/README	2012-09-20 20:16:33 UTC (rev 5941)
+++ SwiftApps/CMTS/scaling/README	2012-09-20 21:05:59 UTC (rev 5942)
@@ -8,21 +8,22 @@
 NAMD simulations.
 
 The user needs to supply the following files:
-NAMD psf file (h0_solvion.psf)
-NAMD pdb file (h0_solvion.pdb)
-CHARMM parameter files (par_all22_prot.inp)
-NAMD coordinate restart file (h0_eq.0.restart.coor)
-NAMD velocity restart file (h0_eq.0.restart.vel)
-NAMD system restart file (h0_eq.0.restart.xsc)
 
+* NAMD psf file (h0_solvion.psf)
+* NAMD pdb file (h0_solvion.pdb)
+* CHARMM parameter files (par_all22_prot.inp)
+* NAMD coordinate restart file (h0_eq.0.restart.coor)
+* NAMD velocity restart file (h0_eq.0.restart.vel)
+* NAMD system restart file (h0_eq.0.restart.xsc)
+
 These files are all located in the input_files directory.
 When the script is run, it creates configuration files
-from the template and then submits an individual job for
-each "number of nodes".
+from the template (input_files/h0_eq.conf) and then submits 
+an individual job for each "number of nodes".
 
 When all of the jobs have run, plot.sh
 will create the data file scale.dat, which will have
-the number of CPUs and days/ns for job. 
+the number of CPUs and days/ns per job. 
 
 Prerequisites
 -------------
@@ -35,6 +36,7 @@
 Grotthuss
 ~~~~~~~~~
 To run on grotthuss, add the following line to $HOME/.bashrc to set the PATH:
+-----
 export PATH=/scratch/davidk/swift-trunk/cog/modules/swift/dist/swift-svn/bin:/Network/Servers/vothfile.uchicago.edu/home/davidk/namd_2.8-intel-openmpi:/Network/Servers/vothfile.uchicago.edu/home/davidk/vmd:/opt/torque/bin:$PATH
 -----